def cli_sleep(data, hypno, config_file, annotations, downsample, use_mne,
preload, show):
"""Open the graphical user interface of Sleep."""
# File conversion :
if data is not None:
data = click.format_filename(data)
if hypno is not None:
hypno = click.format_filename(hypno)
if config_file is not None:
config_file = click.format_filename(config_file)
if annotations is not None:
annotations = click.format_filename(annotations)
s = Sleep(data=data,
hypno=hypno,
downsample=downsample,
use_mne=use_mne,
preload=preload,
config_file=config_file,
annotations=annotations)
if show:
s.show()
"""
Load EDF file
=============
This example demonstrate how to load an EDF file.
Required dataset at :
https://www.dropbox.com/s/bj1ra95rbksukro/sleep_edf.zip?dl=1
.. image:: ../../picture/picsleep/ex_LoadEDF.png
"""
import os
from visbrain import Sleep
from visbrain.io import download_file
current_path = os.getcwd()
target_path = os.path.join(current_path, 'data', 'edf')
download_file('sleep_edf.zip', unzip=True, to_path=target_path)
dfile = os.path.join(target_path, 'excerpt2.edf')
hfile = os.path.join(target_path, 'Hypnogram_excerpt2.txt')
cfile = os.path.join(target_path, 'excerpt2_config.txt')
Sleep(data=dfile, hypno=hfile, config_file=cfile).show()
from visbrain.io import download_file, path_to_visbrain_data
# Get data path and where to save it :
current_path = path_to_visbrain_data()
target_path = os.path.join(current_path, 'sleep_data', 'edf')
# Download the file :
download_file('sleep_edf.zip', unzip=True, to_path=target_path)
# Get data path :
dfile = os.path.join(target_path, 'excerpt2.edf') # data
hfile = os.path.join(target_path, 'Hypnogram_excerpt2.txt') # hypnogram
cfile = os.path.join(target_path, 'excerpt2_config.txt') # GUI config
# Define an instance of Sleep :
sp = Sleep(data=dfile, hypno=hfile, config_file=cfile)
###############################################################################
# Define new methods
###############################################################################
###############################################################################
# Spindle function
# ~~~~~~~~~~~~~~~~
###############################################################################
#
# This function does NOT perform a real spindle detection. It's purpose is to
# show how to replace the default detection behavior by a custom function.
# It just highlights samples between [0, 100], [200, 300] and [400, 500].
import os
from visbrain import Sleep
from glob import glob
import numpy as np
fs = 250
source_dir = r'C:\Users\Rory\raw_data\CIT_WAY\eeg_numpy\CIT_WAY_1_2018-05-01_15-59-19_PRE'
data = np.load(glob(os.path.join(source_dir, '*.npy'))[0])
path_to_txt = glob(os.path.join(source_dir, '*.txt'))[0]
with open(path_to_txt) as f:
labs = np.array(f.read().splitlines())
Sleep(data=data, sf=fs, channels=labs).show()
"""
Load a BrainVision file
=======================
This example demonstrate how to load a BrainVision file.
Required dataset at :
https://drive.google.com/drive/folders/0B6vtJiCQZUBvRjc3cFFYcmFIeW8?usp=sharing
.. image:: ../../picture/picsleep/ex_LoadBrainVision.png
"""
from visbrain import Sleep
Sleep(file='sub-02.eeg', hypno_file='sub-02.hyp',
config_file='sub-02_config.txt').show()
from visbrain import Sleep
from visbrain.io import download_file, path_to_visbrain_data
from visbrain.tests._tests_visbrain import _TestVisbrain
# File to load :
sleep_file = path_to_visbrain_data('excerpt2.edf')
hypno_file = path_to_visbrain_data('Hypnogram_excerpt2.txt')
# Download sleep file :
if not os.path.isfile(sleep_file):
download_file('sleep_edf.zip', unzip=True)
onset = np.array([100, 2000, 5000])
# Create Sleep application :
sp = Sleep(data=sleep_file, hypno=hypno_file, axis=True, annotations=onset)
class TestSleep(_TestVisbrain):
"""Test sleep.py."""
###########################################################################
# TOOLS
###########################################################################
def test_reference_switch(self):
"""Test function reference_switch."""
for k in [2]: # range(3)
sp._ToolsRefMeth.setCurrentIndex(k)
sp._fcn_ref_switch()
sp._fcn_ref_apply()
sp._fcn_ref_chan_ignore()
"""
import os
from mne import io
from visbrain import Sleep
from visbrain.io import download_file, path_to_visbrain_data
###############################################################################
# LOAD YOUR FILE
###############################################################################
current_path = path_to_visbrain_data()
target_path = os.path.join(current_path, 'sleep_data', 'brainvision')
# Download dataset :
download_file("sleep_brainvision.zip", unzip=True, to_path=target_path)
dfile = os.path.join(target_path, 'sub-02.vhdr')
hfile = os.path.join(target_path, 'sub-02.hyp')
# Read raw data using MNE-python :
raw = io.read_raw_brainvision(vhdr_fname=dfile, preload=True)
# Extract data, sampling frequency and channels names
data, sf, chan = raw._data, raw.info['sfreq'], raw.info['ch_names']
# Now, pass all the arguments to the Sleep module :
Sleep(data=data, sf=sf, channels=chan, hypno=hfile).show()
# Alternatively, these steps can be done automatically by using the 'use_mne'
# input argument of sleep
# Sleep(data=dfile, hypno=hfile, use_mne=True).show()
.. image:: ../../picture/picsleep/ex_LoadMatlab.png
"""
import os
import numpy as np
from scipy.io import loadmat
from visbrain import Sleep
from visbrain.io import download_file, path_to_visbrain_data
###############################################################################
# LOAD YOUR FILE
###############################################################################
current_path = path_to_visbrain_data()
target_path = os.path.join(current_path, 'sleep_data', 'matlab')
# Download matlab file :
download_file("sleep_matlab.zip", unzip=True, to_path=target_path)
# Load the matlab file :
mat = loadmat(os.path.join(target_path, 's2_sleep.mat'))
# Get the data, sampling frequency and channel names :
raw_data = mat['data']
raw_sf = float(mat['sf'])
raw_channels = np.concatenate(mat['channels'].flatten()).tolist()
raw_hypno = mat['hypno'].flatten()
# Open the GUI :
Sleep(data=raw_data, sf=raw_sf, channels=raw_channels, hypno=raw_hypno).show()
# Create a random dataset :
sf, nelec, npts = 1000., 8, 100000
data = 10. * np.random.rand(nelec, npts)
channels = ['Cz', 'Fz', 'C1', 'C2', 'C3', 'C4', 'F1', 'other']
hypno = np.random.randint(-1, 3, (npts, ))
file, hypno_file = None, None
onset = np.array([100, 2000, 5000])
# Create Sleep application :
app = QtWidgets.QApplication([])
sp = Sleep(file=file,
hypno_file=hypno_file,
data=data,
channels=channels,
sf=sf,
downsample=100.,
hypno=hypno,
axis=False,
hedit=True,
annotation_file=onset)
class TestSleep(object):
"""Test sleep.py."""
###########################################################################
# SETTINGS
###########################################################################
def test_create_tmp_folder(self):
"""Create tmp folder."""
if not os.path.exists(path_to_tmp):
""" Load a file using MNE-python ============================ This example shows how to load data using MNE-Python package. https://martinos.org/mne/stable/index.html Install MNE-python : pip install mne A full list of supported format can be found here: https://martinos.org/mne/stable/python_reference.html#reading-raw-data Required dataset at : https://drive.google.com/drive/folders/0B6vtJiCQZUBvRjc3cFFYcmFIeW8?usp=sharing .. image:: ../../picture/picsleep/ex_LoadMNE.png """ from mne import io from visbrain import Sleep raw = io.read_raw_brainvision(vhdr_fname='sub-02.vhdr', preload=True) # Extract data, sampling frequency and channels names data, sf, chan = raw._data, raw.info['sfreq'], raw.info['ch_names'] # Now, pass all the arguments to the Sleep module : Sleep(data=data, sf=sf, channels=chan, hypno_file='sub-02.hyp').show()
"""
Load ELAN files
===============
This example demonstrate how to load an ELAN file.
Required dataset at :
https://www.dropbox.com/s/95xvdqivpgk90hg/sleep_elan.zip?dl=1
.. image:: ../../picture/picsleep/ex_LoadElan.png
"""
import os
from visbrain import Sleep
from visbrain.io import download_file
current_path = os.getcwd()
target_path = os.path.join(current_path, 'data', 'elan')
# Download dataset :
download_file("sleep_elan.zip", unzip=True, to_path=target_path)
dfile = os.path.join(target_path, 'sub-02.eeg')
hfile = os.path.join(target_path, 'sub-02.hyp')
Sleep(data=dfile, hypno=hfile).show()
==============
This example demonstrate how to load a .rec file.
Required dataset at :
https://www.dropbox.com/s/hc18bgn2hlnmiph/sleep_edf.zip?dl=1
.. image:: ../../picture/picsleep/ex_load_rec.png
"""
import os
from visbrain import Sleep
from visbrain.io import download_file, path_to_visbrain_data
###############################################################################
# LOAD YOUR FILE
###############################################################################
current_path = path_to_visbrain_data()
target_path = os.path.join(current_path, 'sleep_data', 'rec')
# Download the rec file :
download_file('sleep_rec.zip',
unzip=True,
to_path=target_path,
remove_archive=True)
dfile = os.path.join(target_path, '1.rec')
# Open the GUI :
Sleep(data=dfile).show()
"""
Load a Matlab file
==================
This example demonstrate how to load an ELAN file.
Required dataset at :
https://drive.google.com/drive/folders/0B6vtJiCQZUBvRjc3cFFYcmFIeW8?usp=sharing
.. image:: ../../picture/picsleep/ex_LoadMatlab.png
"""
from visbrain import Sleep
import numpy as np
from scipy.io import loadmat
mat = loadmat('s2_sleep.mat')
# Get the data, sampling frequency and channel names :
raw_data = mat['data']
raw_sf = float(mat['sf'])
raw_channels = np.concatenate(mat['channels'].flatten()).tolist()
raw_hypno = mat['hypno'].flatten()
Sleep(data=raw_data, sf=raw_sf, channels=raw_channels, hypno=raw_hypno,
config_file='s2_config.txt').show()
"""
Load ELAN files
===============
This example demonstrate how to load an ELAN file.
Required dataset at :
https://drive.google.com/drive/folders/0B6vtJiCQZUBvRjc3cFFYcmFIeW8?usp=sharing
.. image:: ../../picture/picsleep/ex_LoadElan.png
"""
from visbrain import Sleep
Sleep(file='s101_sleep.eeg',
hypno_file='s101_hypno.hyp',
config_file='s101_config.txt').show()
"""
Load EDF file
=============
This example demonstrate how to load an EDF file.
Required dataset at :
https://drive.google.com/drive/folders/0B6vtJiCQZUBvRjc3cFFYcmFIeW8?usp=sharing
.. image:: ../../picture/picsleep/ex_LoadEDF.png
"""
from visbrain import Sleep
Sleep(file='excerpt2.edf', hypno_file='Hypnogram_excerpt2.txt',
config_file='excerpt2_config.txt').show()